Research progress on single-cell expression quantitative trait loci.

Expression quantitative trait loci (eQTL) represent genetic variants that regulate gene expression levels. eQTL analysis has become a crucial method for identifying the functional roles of disease-associated genetic variants in the post-genome-wide association study (GWAS) era, yielding numerous significant discoveries. Traditional eQTL analysis relies on whole-genome sequencing combined with bulk RNA-seq, which obscures gene expression differences between cells and thus fails to identify cell type- or state-dependent eQTL. This limitation makes it challenging to elucidate the roles of disease-associated genetic variants under specific conditions. In recent years, with the development and widespread application of single-cell RNA sequencing (scRNA-seq) technology, scRNA-seq-based eQTL (sc-eQTL) research has emerged as a focal point. The advantage of this approach lies in its ability to leverage the resolution and granularity of single-cell sequencing to uncover eQTL that are dependent on cell type, cell state, and cellular dynamics. This significantly enhances our ability to analyze genetic variants associated with gene expression. Consequently, it holds substantial significance for advancing our understanding of the formation of complex organs and the mechanisms underlying disease onset, progression, intervention, and treatment. This review comprehensively examines the recent advancements in sc-eQTL studies, focusing on their development, experimental design strategies, modeling approaches, and current challenges. The aim is to offer researchers novel perspectives for identifying disease-associated loci and elucidating gene regulatory mechanisms.

[A comprehensive repository of mutation data and a clinical assistant decision system for hemoglobinopathy in the Chinese population].

Personal genomic information benefits from accumulated big data and its application is no longer limited to scientific research. Presently, it is undergoing the transformation to daily medical practice. Systematic arrangement, archiving and rational utilization of disease-related genomic information is an important foundation of future precision medicine. Hemoglobinopathy is prevalent in southern China, but its molecular pathological basis has racial specificity. To facilitate clinical diagnosis and genetic screening of hemoglobinopathy in southern China, we established the LOVD gene data management system for the variation and phenotype spectrum of hemoglobinopathy. Then we designed an integrated and efficient on-line auxiliary accurate diagnosis and risk assessment system in order to assist clinicians to make comprehensive diagnosis and genetic counseling in a short time based on cloud standardized annotated library of specific hemoglobinopathy variants and diagnostic repository. The methodology and experience of improving the clinical decision-making efficiency of diseases with big data and artificial intelligence technology can be used as an example in the clinical and preventive application of other diseases.

A novel C-type lectin from the shrimp Litopenaeus vannamei possesses anti-white spot syndrome virus activity.

C-type lectins play key roles in pathogen recognition, innate immunity, and cell-cell interactions. Here, we report a new C-type lectin (C-type lectin 1) from the shrimp Litopenaeus vannamei (LvCTL1), which has activity against the white spot syndrome virus (WSSV). LvCTL1 is a 156-residue polypeptide containing a C-type carbohydrate recognition domain with an EPN (Glu(99)-Pro(100)-Asn(101)) motif that has a predicted ligand binding specificity for mannose. Reverse transcription-PCR analysis revealed that LvCTL1 mRNA was specifically expressed in the hepatopancreas of L. vannamei. Recombinant LvCTL1 (rLvCTL1) had hemagglutinating activity and ligand binding specificity for mannose and glucose. rLvCTL1 also had a strong affinity for WSSV and interacted with several envelope proteins of WSSV. Furthermore, we showed that the binding of rLvCTL1 to WSSV could protect shrimps from viral infection and prolong the survival of shrimps against WSSV infection. Our results suggest that LvCTL1 is a mannose-binding C-type lectin that binds to envelope proteins of WSSV to exert its antiviral activity. To our knowledge, this is the first report of a shrimp C-type lectin that has direct anti-WSSV activity.

HMGB1 Promotes the Proliferation and Metastasis of Lung Cancer by Activating the Wnt/ß-Catenin Pathway.

The aim of this study was to investigate the role of high mobility group protein-1 (HMGB1) in the proliferation and migration of lung cancer cells. CCK-8 assays and colony formation assays were used to evaluate the effect of HMGB1 regulation on cancer cell viability and colony formation. Trans-well assays and wound healing assays were also performed. Our data showed that HMGB1 is upregulated in clinical lung cancer tissues compared with non-cancer tissues, and it is differentially expressed in lung cancer cell lines. The knockdown of HMGB1 in A549 lung cancer cells significantly reduced cell proliferation, viability and motility. In contrast, overexpression of HMGB1 in lung cancer H1299 cells significantly increased cell viability and motility. Western blotting showed that HMGB1 could promote epithelial-mesenchymal transition. The Wnt/ß-catenin pathway was activated after overexpression of HMGB1 in H1299 cells, while it was inactivated by knocking down HMGB1 in A549 cells. These data suggest that HMGB1 promotes the proliferation and migration of lung cancer cells in vitro. The carcinogenic behavior of HMGB1 can be achieved by activating the Wnt/ß-catenin pathway.

SIRT7 activates p53 by enhancing PCAF-mediated MDM2 degradation to arrest the cell cycle.

Sirtuin 7 (SIRT7), an NAD+-dependent deacetylase, plays vital roles in energy sensing, but the underlying mechanisms of action remain less clear. Here, we report that SIRT7 is required for p53-dependent cell-cycle arrest during glucose deprivation. We show that SIRT7 directly interacts with p300/CBP-associated factor (PCAF) and the affinity for this interaction increases during glucose deprivation. Upon binding, SIRT7 deacetylates PCAF at lysine 720 (K720), which augments PCAF binding to murine double minute (MDM2), the p53 E3 ubiquitin ligase, leading to accelerated MDM2 degradation. This effect results in upregulated expression of the cell-cycle inhibitor, p21Waf1/Cip1, which further leads to cell-cycle arrest and decreased cell viability. These data highlight the importance of the SIRT7-PCAF interaction in regulating p53 activity and cell-cycle progression during conditions of glucose deprivation. This axis may represent a new avenue to design effective therapeutics based on tumor starvation.

Infectious spleen and kidney necrosis virus ORF48R functions as a new viral vascular endothelial growth factor.

Infectious spleen and kidney necrosis virus (ISKNV) causes a pandemic and serious disease in fish. Infection by ISKNV causes epidermal lesions, in which petechial hemorrhages and abdominal edema are prominent features. ISKNV ORF48R contains a domain similar to that of the platelet-derived growth factor and vascular endothelial growth factor (VEGF) families of proteins. ISKNV ORF48R showed higher similarity to the VEGFs encoded by Megalocytivirus and Parapoxvirus than to those encoded in fish and mammals. We used zebrafish as a model and constructed a recombinant plasmid containing the DNA sequence of ISKNV ORF48R to study ISKNV infection. The plasmid was microinjected into zebrafish embryos at the one-cell stage. Overexpression of the ISKNV ORF48R gene results in pericardial edema and dilation at the tail region of zebrafish embryos, suggesting that ISKNV ORF48R induces vascular permeability. ISKNV ORF48R is also able to stimulate a striking expression of flk1 in the zebrafish dorsal aorta and the axial vein. Furthermore, ISKNV ORF48R, while cooperating with zebrafish VEGF(121), can stimulate more striking expression of flk1 than can either ISKNV ORF48R or zebrafish VEGF(121) alone. However, decreased expression of FLK-1 by gene knockdown results in the disappearance of pericardial edema and dilation at the tail region of zebrafish embryos induced by overexpression of ISKNV ORF48R in the early stages of embryonic development.

USP4 positively regulates RLR-induced NF-κB activation by targeting TRAF6 for K48-linked deubiquitination and inhibits enterovirus 71 replication.

Retinoic acid-inducible gene I-like receptor (RLR) is one of the most important pattern recognition receptors of the innate immune system that detects positive and/or negative stranded RNA viruses. Subsequently, it stimulates downstream transcription of interferon regulatory factor 3 (IRF3) and nuclear factor κB (NF-κB) inducing the production of interferons (IFNs) and inflammatory cytokines. Tumour necrosis factor receptor associated factor 6 (TRAF6) is a key protein involved in the RLR-mediated antiviral signalling pathway, recruiting additional proteins to form a multiprotein complex capable of activating the NF-κB inflammatory pathway. Despite TRAF6 playing an important role in regulating host immunity and viral infection, the deubiquitination of TRAF6 induced by viral infection remains elusive. In this study, we found that enterovirus 71 (EV71) infection attenuated the expression of Ubiquitin-specific protease 4 (USP4) in vitro and in vivo, while overexpression of USP4 significantly suppressed EV71 replication. Furthermore, it was found that EV71 infection reduced the RLR signalling pathway and enhanced the degradation of TRAF6. USP4 was also found to interact with TRAF6 and positively regulate the RLR-induced NF-κB signalling pathway, inhibiting the replication of EV71. Therefore, as a novel positive regulator of TRAF6, USP4 plays an essential role in EV71 infection by deubiquitinating K48-linked ubiquitin chains.

[Particle Size Distribution and Human Health Risk Assessment of Heavy Metals in Atmospheric Particles from Beijing and Xinxiang During Summer].

Under a condition of good air quality (AQI:55-90, PM10:37-97 µg·m-3, PM2.5:17-76 µg·m-3), six groups of 54 samples were collected using an Andersen cascade impactor from both the indoor and outdoor stations in Beijing and Xinxiang from June to August in 2016. The samples were digested by microwave digestion, and nine heavy metal elements (Pb, Cr, Ni, Cu, Zn, As, Cd, Mn, and Co) in the atmospheric particles were determined with an inductively coupled plasma source mass spectrometer (ICP-MS). The results showed that the enrichment index (0-3) of most elements were low in both cities except for Cd[15.0 (Beijing) and 8.47 (Xinxiang)]. Cr, Co, Cu, and Mn in the atmospheric particles from Beijing park, Cd, Pb, and Mn in the atmospheric particles from the Beijing office, Cr, Co, Ni, and As in the atmospheric particles from Xinxiang park, and all nine heavy metal elements in the atmospheric particles from roads in both cities were found to be more concentrated in the coarse fractions; however, Pb, Zn, Cd, Ni, and As in the atmospheric particles from Beijing park, Co, Zn, Ni, Cr, As, and Cu in the atmospheric particles from the Beijing office, Pb, Zn, Cd, Cu, and Mn in the atmospheric particles from Xinxiang park, and all nine metal elements in the atmospheric particles from the Beijing office showed the opposite pattern. The result of a human health risk assessment indicated that the carcinogenic risk of the five carcinogenic elements were all less than 10-4, but a lower potential cancer risk would also occur under long term exposure. For the four non-carcinogenic elements (Pb, Zn, Mn, and Cu), the non-carcinogenic health risk values of Pb, Zn, Mn, and Cu in the atmospheric particulates in Beijing were all far less than 1, which means the corresponding non-carcinogenic risk was negligible; and, except for Mn, there was no obvious non-carcinogenic risk from Pb, Zn, and Cu in the atmospheric particles of Xinxiang.

Litopenaeus vannamei NF-κB is required for WSSV replication.

Many viruses can hijack the host cell NF-κB as part of their life cycle, diverting NF-κB immune regulatory functions to favor their replications. There were several reports on the functions of Litopenaeus vannamei NF-κB (LvNF-κB) in White spot syndrome virus (WSSV) replication in vitro. Here, we studied the relationship between LvNF-κB family protein Dorsal (LvDorsal) and Relish (LvRelish) with WSSV replication in vivo. The expressions of LvDorsal and LvRelish were significantly upregulated by WSSV challenge. Virus loads and expression of viral envelope protein VP28 in LvDorsal or LvRelish silencing shrimps were significantly lower than the control shrimps injected with EGFP-dsRNA or PBS after challenge with 1×10(5) copies WSSV/shrimp. In addition to the LvDorsal activation of WSV069 (ie1) and WSV303 promoter that we have reported, LvRelish can also activate WSV069 (ie1) and WSV303 promoter by dual luciferase reporter assays through screening 40 WSSV gene promoters that have putative multiple NF-κB binding sites. The promoter activity of the WSV069 (ie1) by LvDorsal activation was significantly higher than that by LvRelish activation. WSSV replication in LvDorsal, LvRelish or WSV303 silencing shrimps were significantly inhibited. These results indicate that the L. vannamei NF-κB family proteins LvDorsal and LvRelish expressions are significantly activated by WSSV challenge and WSSV replication partially relied on the activations of LvDorsal and LvRelish in vivo.

Shrimp NF-κB binds to the immediate-early gene ie1 promoter of white spot syndrome virus and upregulates its activity.

The immediate-early gene ie1 carried by white spot syndrome virus (WSSV) exhibits very strong promoter activity and expresses highly throughout the infection cycle. Here we identified a NF-κB binding motif in the ie1 promoter region. Electrophoretic mobility shift assays indicated that the recombinant Rel homology domain (RHD) of shrimp NF-κB homolog LvRelish bound to the putative NF-κB site in the ie1 promoter. A transactivity assay of the WSSV ie1 promoter in Drosophila Schneider 2 cells demonstrated that LvRelish could increase ie1 promoter activity. These results show that shrimp NF-κB homolog LvRelish transactivates WSSV ie1 gene expression and contributes to its high promoter activity. Further transactivation assays showed that WSSV IE1 protein expression upregulated the promoter activities of WSSV ie1 gene and antimicrobial peptide genes regulated by the NF-κB system. We suggested that WSSV may annex the shrimp NF-κB system, which it uses to enhance the expression of viral immediate-early genes.